SMTL ID : 7niy.1

E. coli NfsA with FMN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.03 Å

Oligo State

homo-dimer

Ligands

4 x HQE: benzene-1,4-diol(Covalent)

HQE.1: 5 residues within 4Å: Chain A: C.9 Chain B: N.32, R.35, A.36 Ligands: IMD.7 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.32, B:A.36 HQE.2: 5 residues within 4Å: Chain A: C.90, P.91, D.92 Chain B: R.217, I.221 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:R.217, B:I.221 Hydrogen bonds: A:D.92 Water bridges: A:D.92 HQE.10: 5 residues within 4Å: Chain A: N.32, R.35, A.36 Chain B: C.9 Ligands: IMD.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.32, A:A.36 HQE.11: 5 residues within 4Å: Chain A: R.217, I.221 Chain B: C.90, P.91, D.92 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:R.217, A:I.221 Hydrogen bonds: B:D.92 Water bridges: B:D.92

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.3: 21 residues within 4Å: Chain A: S.38, S.39, S.40, F.42, V.106, D.107, M.110 Chain B: H.11, R.12, S.13, R.15, Q.67, H.69, V.127, Y.128, I.129, G.130, G.131, K.167, R.169 Ligands: FMN.5 22 PLIP interactions: 18 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.128, B:Y.128, A:V.106 Hydrogen bonds: B:S.13, B:S.13, B:S.13, B:R.15, B:Q.67, B:Q.67, B:G.130, B:G.131, B:K.167, A:S.38, A:S.39 Water bridges: B:R.15, B:R.15, B:R.169, B:R.169, A:S.38 Salt bridges: B:H.11, B:K.167, B:R.169 FMN.5: 12 residues within 4Å: Chain A: S.41 Chain B: R.15, G.65, Q.67, G.131, K.167, Y.200, R.203, R.208, R.225 Ligands: FMN.3, CL.6 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Q.67 Hydrogen bonds: B:Y.199, B:Y.200, B:R.225, A:S.41 Water bridges: B:K.167, B:K.167, B:R.208, B:R.208 Salt bridges: B:K.167, B:R.203, B:R.208 FMN.12: 21 residues within 4Å: Chain A: H.11, R.12, S.13, R.15, Q.67, H.69, V.127, Y.128, I.129, G.130, G.131, K.167, R.169 Chain B: S.38, S.39, S.40, F.42, V.106, D.107, M.110 Ligands: FMN.14 22 PLIP interactions: 18 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.128, A:Y.128, B:V.106 Hydrogen bonds: A:S.13, A:S.13, A:S.13, A:R.15, A:Q.67, A:Q.67, A:G.130, A:G.131, A:K.167, B:S.38, B:S.39 Water bridges: A:R.15, A:R.15, A:R.169, A:R.169, B:S.38 Salt bridges: A:H.11, A:K.167, A:R.169 FMN.14: 12 residues within 4Å: Chain A: R.15, G.65, Q.67, G.131, K.167, Y.200, R.203, R.208, R.225 Chain B: S.41 Ligands: FMN.12, CL.15 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Q.67 Hydrogen bonds: A:R.225, B:S.41 Water bridges: A:K.167, A:K.167, A:R.208, A:R.208 Salt bridges: A:K.167, A:R.203, A:R.208

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 8 residues within 4Å: Chain A: F.83, L.95, G.96, L.97, Q.100, H.148, G.236, W.237 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.96, A:L.97, A:Q.100, A:H.148 EDO.9: 7 residues within 4Å: Chain A: A.34, R.35, T.37, S.39, Q.44, M.111 Chain B: R.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.37 EDO.13: 8 residues within 4Å: Chain B: F.83, L.95, G.96, L.97, Q.100, H.148, G.236, W.237 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.96, B:L.97, B:Q.100, B:H.148 EDO.18: 7 residues within 4Å: Chain A: R.169 Chain B: A.34, R.35, T.37, S.39, Q.44, M.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.37

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain B: G.130, R.225 Ligands: FMN.5 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: G.130, R.225 Ligands: FMN.14 Ligand excluded by PLIP

4 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 4 residues within 4Å: Chain A: C.9, L.166, K.167 Ligands: HQE.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.9 IMD.8: 2 residues within 4Å: Chain A: E.20, W.159 2 PLIP interactions: 2 interactions with chain A pi-Stacking: A:W.159, A:W.159 IMD.16: 4 residues within 4Å: Chain B: C.9, L.166, K.167 Ligands: HQE.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.9 IMD.17: 2 residues within 4Å: Chain B: E.20, W.159 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.20 pi-Stacking: B:W.159, B:W.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Day, M.A. et al., The structures of E. coli NfsA bound to the antibiotic nitrofurantoin; to 1,4-benzoquinone and to FMN. Biochem.J. (2021)

Release Date

2021-07-21

Peptides

Oxygen-insensitive NADPH nitroreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Oxygen-insensitive NADPH nitroreductase

Related Entries With Identical Sequence